Development of SNP markers for C57BL/6N-derived mouse inbred strains

Abstract

C57BL/6N inbred mice are used as the genetic background for producing knockout mice in large-scale projects worldwide; however, the genetic divergence among C57BL/6N-derived substrains has not been verified. Here, we identified novel single nucleotide polymorphisms (SNPs) specific to the C57BL/6NJ strain and selected useful SNPs for the genetic monitoring of C57BL/6N-derived substrains. Informative SNPs were selected from the public SNP database at the Wellcome Trust Sanger Institute by comparing sequence data from C57BL/6NJ and C57BL/6J mice. A total of 1,361 candidate SNPs from the SNP database could distinguish the C57BL/6NJ strain from 12 other inbred strains. We confirmed 277 C57BL/6NJ-specific SNPs including 10 nonsynonymous SNPs by direct sequencing, and selected 100 useful SNPs that cover all of the chromosomes except Y. Genotyping of 11 C57BL/6N-derived substrains at these 100 SNP loci demonstrated genetic differences among the substrains. This information will be useful for accurate genetic monitoring of mouse strains with a C57BL/6N-derived background.

Fig. 1.

Genealogy of C57BL/6N-derived substrains (left) and a bar graph for the number of C57BL/6NJ-specific SNPs (single nucleotide polymorphisms) (right). Abbreviations in the genealogy: N: National Institutes of Health; By: Dr. Donald Bailey; J: The Jackson Laboratory; Cr: National Cancer Institute; Jms: Institute of Medical Science, The University of Tokyo; Slc: Japan SLC; Crl: Charles River Laboratories; Crlj: Charles River Laboratories Japan; Seac: Kyudo; Hsd: Harlan Laboratories; Jic: Central Institute for Experimental Animals; Jcl: CLEA Japan; Sim: Simonsen Laboratories; Tac: Taconic Farm. Doted line: the year of introduction was unknown. Broken line: the strain was stored as frozen embryos. The C57BL/6NHsd and C57BL/6NCrl strains were derived independently from the NIH on unknown dates in 1974. On the right (bar graph), the number of C57BL/6NJ-specific SNPs of each C57BL/6N-derived substrain is indicated as a solid bar. The number of SNPs is also indicated at the right side of each bar.